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Xu C, Li J, Song LY, Guo ZJ, Song SW, Zhang LD, Zheng HL. PlantC2U: deep learning of cross-species sequence landscapes predicts plastid C-to-U RNA editing in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2266-2279. [PMID: 38190348 DOI: 10.1093/jxb/erae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/07/2024] [Indexed: 01/10/2024]
Abstract
In plants, C-to-U RNA editing mainly occurs in plastid and mitochondrial transcripts, which contributes to a complex transcriptional regulatory network. More evidence reveals that RNA editing plays critical roles in plant growth and development. However, accurate detection of RNA editing sites using transcriptome sequencing data alone is still challenging. In the present study, we develop PlantC2U, which is a convolutional neural network, to predict plastid C-to-U RNA editing based on the genomic sequence. PlantC2U achieves >95% sensitivity and 99% specificity, which outperforms the PREPACT tool, random forests, and support vector machines. PlantC2U not only further checks RNA editing sites from transcriptome data to reduce possible false positives, but also assesses the effect of different mutations on C-to-U RNA editing based on the flanking sequences. Moreover, we found the patterns of tissue-specific RNA editing in the mangrove plant Kandelia obovata, and observed reduced C-to-U RNA editing rates in the cold stress response of K. obovata, suggesting their potential regulatory roles in plant stress adaptation. In addition, we present RNAeditDB, available online at https://jasonxu.shinyapps.io/RNAeditDB/. Together, PlantC2U and RNAeditDB will help researchers explore the RNA editing events in plants and thus will be of broad utility for the plant research community.
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Affiliation(s)
- Chaoqun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ling-Yu Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ze-Jun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Shi-Wei Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Lu-Dan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
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2
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Hou Q, Shang L, Chen X, Luo Q, Wei L, Zhang C. Convergent evolution of allele-specific gene expression that leads to non-small cell lung cancer in different human populations. J Appl Genet 2023:10.1007/s13353-023-00813-4. [PMID: 38036772 DOI: 10.1007/s13353-023-00813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
Phenotypical innovations during evolution are caused by novel mutations, which are usually heterozygous at the beginning. The gene expressions on two alleles of these mutation sites are not necessarily identical, leading to flexible allele-specific regulation in cell systems. We retrieve the transcriptome data of normal and non-small cell lung cancer (NSCLC) tissues from 47 African Americans (AA) and 50 European Americans (EA). We analyze the differentially expressed genes (DEGs) in NSCLC as well as the tumor-specific mutations. Expression and mutation profiles show convergent evolution in AA and EA populations. The tumor-specific mutations are poorly overlapped, but many of them are located in the same genes, mainly oncogenes and tumor suppressor genes. The DEGs in tumors are majorly caused by the mutated alleles rather than normal alleles. The relative expressions of mutated alleles are highly correlated between AA and EA. The differential expression in NSCLC is predominantly mediated by the mutated alleles on heterozygous sites. This molecular mechanism underlying NSCLC oncogenesis is conserved across different human populations, exhibiting convergent evolution. We present this novel angle that differential expression analysis should be performed separately for different alleles. Our ideas should greatly benefit the cancer community.
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Affiliation(s)
- Qiuyu Hou
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Lifeng Shang
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Xu Chen
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Qiang Luo
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Liang Wei
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Chence Zhang
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China.
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3
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Ge F, Cao X, Jiang Y. A-to-I RNA editing shows dramatic up-regulation in osteosarcoma and broadly regulates tumor-related genes by altering microRNA target regions. J Appl Genet 2023; 64:493-505. [PMID: 37542613 DOI: 10.1007/s13353-023-00777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
A-to-I RNA editing is a prevalent type of RNA modification in animals. The dysregulation of RNA editing has led to multiple human cancers. However, the role of RNA editing has never been studied in osteosarcoma, a complex bone cancer with unknown molecular basis. We retrieved the RNA-sequencing data from 24 primary osteosarcoma patients and 3 healthy controls. We systematically profiled the RNA editomes in these samples and quantitatively identified reliable differential editing sites (DES) between osteosarcoma and normal samples. RNA editing efficiency is dramatically increased in osteosarcoma, presumably due to the significant up-regulation of editing enzymes ADAR1 and ADAR2. Up-regulated DES in osteosarcoma are enriched in 3'UTRs. Strikingly, such 3'UTR sites are further enriched in microRNA binding regions of gene EMP2 and other oncogenes, abolishing the microRNA suppression on target genes. Accordingly, the expression of these tumor-promoting genes is elevated in osteosarcoma. There might be an RNA editing-dependent pathway leading to osteosarcoma. We expanded our knowledge on the potential roles of RNA editing in oncogenesis. Based on these molecular features, our work is valuable for future prognosis and diagnosis of osteosarcoma.
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Affiliation(s)
- Fuqun Ge
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Xinyue Cao
- School of Clinical Medicine, Qilu Medical University, Zibo, 255300, Shandong, China
| | - Yankai Jiang
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China.
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4
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Li Y, Hou F, Zhou M, Yang X, Yin B, Jiang W, Xu H. C-to-U RNA deamination is the driving force accelerating SARS-CoV-2 evolution. Life Sci Alliance 2023; 6:6/1/e202201688. [PMID: 36347544 PMCID: PMC9644418 DOI: 10.26508/lsa.202201688] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
Understanding the molecular mechanism underlying the rampant mutation of SARS-CoV-2 would help us control the COVID-19 pandemic. The APOBEC-mediated C-to-U deamination is a major mutation type in the SARS-CoV-2 genome. However, it is unclear whether the novel mutation rate u is higher for C-to-U than for other mutation types, and what the detailed driving force is. By analyzing the time course SARS-CoV-2 global population data, we found that C-to-U has the highest novel mutation rate u among all mutation types and that this u is still increasing with time (du/dt > 0). Novel C-to-U events, rather than other mutation types, have a preference over particular genomic regions. A less local RNA structure is correlated with a high novel C-to-U mutation rate. A cascade model nicely explains the du/dt > 0 for C-to-U deamination. In SARS-CoV-2, the RNA structure serves as the molecular basis of the extremely high and continuously accelerating C-to-U deamination rate. This mechanism is the driving force of the mutation, adaptation, and evolution of SARS-CoV-2. Our findings help us understand the dynamic evolution of the virus mutation rate.
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Affiliation(s)
- Yan Li
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, China
| | - Fanghua Hou
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, China
| | - Meili Zhou
- Emergency Department, Qingdao Center Hospital, Qingdao, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Huiqing Xu
- Department of Pathology, Qingdao Haici Hospital, Qingdao, China
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5
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Zhang M, Li Z, Wang Z, Xiao Y, Bao L, Wang M, An C, Gao Y. Exploring the RNA Editing Events and Their Potential Regulatory Roles in Tea Plant ( Camellia sinensis L.). Int J Mol Sci 2022; 23:13640. [PMID: 36362430 PMCID: PMC9654872 DOI: 10.3390/ijms232113640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 04/11/2024] Open
Abstract
RNA editing is a post-transcriptional modification process that alters the RNA sequence relative to the genomic blueprint. In plant organelles (namely, mitochondria and chloroplasts), the most common type is C-to-U, and the absence of C-to-U RNA editing results in abnormal plant development, such as etiolation and albino leaves, aborted embryonic development and retarded seedling growth. Here, through PREP, RES-Scanner, PCR and RT-PCR analyses, 38 and 139 RNA editing sites were identified from the chloroplast and mitochondrial genomes of Camellia sinensis, respectively. Analysis of the base preference around the RNA editing sites showed that in the -1 position of the edited C had more frequent occurrences of T whereas rare occurrences of G. Three conserved motifs were identified at 25 bases upstream of the RNA editing site. Structural analyses indicated that the RNA secondary structure of 32 genes, protein secondary structure of 37 genes and the three-dimensional structure of 5 proteins were altered due to RNA editing. The editing level analysis of matK and ndhD in six tea cultivars indicated that matK-701 might be involved in the color change of tea leaves. Furthermore, 218 PLS-CsPPR proteins were predicted to interact with the identified RNA editing sites. In conclusion, this study provides comprehensive insight into RNA editing events, which will facilitate further study of the RNA editing phenomenon of the tea plant.
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Affiliation(s)
- Mengyuan Zhang
- College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhuo Li
- College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zijian Wang
- College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yao Xiao
- College of Language and Culture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Lu Bao
- College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Min Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chuanjing An
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuefang Gao
- College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China
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Manna PR, Gray ZC, Sikdar M, Reddy H. COVID-19 and its genomic variants: Molecular pathogenesis and therapeutic interventions. EXCLI JOURNAL 2022; 21:1196-1221. [PMID: 36381644 PMCID: PMC9650701 DOI: 10.17179/excli2022-5315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022]
Abstract
Coronavirus disease-19 (COVID-19), caused by a β-coronavirus and its genomic variants, is associated with substantial morbidities and mortalities globally. The COVID-19 virus and its genomic variants enter host cells upon binding to the angiotensin converting enzyme 2 receptors that are expressed in a variety of tissues, but predominantly in the lungs, heart, and blood vessels. Patients afflicted with COVID-19 may be asymptomatic or present with critical symptoms possibly due to diverse lifestyles, immune responses, aging, and underlying medical conditions. Geriatric populations, especially men in comparison to women, with immunocompromised conditions, are most vulnerable to severe COVID-19 associated infections, complications, and mortalities. Notably, whereas immunomodulation, involving nutritional consumption, is essential to protecting an individual from COVID-19, immunosuppression is detrimental to a person with this aggressive disease. As such, immune health is inversely correlated to COVID-19 severity and resulting consequences. Advances in genomic and proteomic technologies have helped us to understand the molecular events underlying symptomatology, transmission and, pathogenesis of COVID-19 and its genomic variants. Accordingly, there has been development of a variety of therapeutic interventions, ranging from mask wearing to vaccination to medication. This review summarizes the current understanding of molecular pathogenesis of COVID-19, effects of comorbidities on COVID-19, and prospective therapeutic strategies for the prevention and treatment of this contagious disease.
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Affiliation(s)
- Pulak R. Manna
- Department of Internal Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79430, USA,*To whom correspondence should be addressed: Pulak R. Manna, Department of Internal Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79430, USA; Tel: +1-806-743-3573, Fax: +1-806-743-3143, E-mail:
| | - Zackery C. Gray
- Department of Internal Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79430, USA
| | - Malabika Sikdar
- Department of Zoology, Dr. Hari Singh Gour Vishwavidyalaya, Sagar, MP 470003, India
| | - Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79430, USA,Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA,Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA,Public Health Department of the Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA,Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA,Nutritional Sciences Department, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA
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7
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Wan J, Wang Q, Zhao J, Zhang X, Guo Z, Hu D, Meng S, Lin Y, Qiu X, Mu L, Ding D, Tang J. Gene expression variation explains maize seed germination heterosis. BMC PLANT BIOLOGY 2022; 22:301. [PMID: 35718761 PMCID: PMC9208091 DOI: 10.1186/s12870-022-03690-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Heterosis has been extensively utilized in plant breeding, however, the underlying molecular mechanism remains largely elusive. Maize (Zea mays), which exhibits strong heterosis, is an ideal material for studying heterosis. RESULTS In this study, there is faster imbibition and development in reciprocal crossing Zhengdan958 hybrids than in their parent lines during seed germination. To investigate the mechanism of heterosis of maize germination, comparative transcriptomic analyses were conducted. The gene expression patterns showed that 1324 (47.27%) and 1592 (66.44%) of the differential expression genes between hybrids and either parental line display parental dominance up or higher levels in the reciprocal cross of Zhengdan958, respectively. Notably, these genes were mainly enriched in metabolic pathways, including carbon metabolism, glycolysis/gluconeogenesis, protein processing in endoplasmic reticulum, etc. CONCLUSION: Our results provide evidence for the higher expression level genes in hybrid involved in metabolic pathways acting as main contributors to maize seed germinating heterosis. These findings provide new insights into the gene expression variation of maize embryos and improve the understanding of maize seed germination heterosis.
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Affiliation(s)
- Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiawen Zhao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Desheng Hu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, China.
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Cai H, Liu X, Zheng X. RNA editing detection in SARS-CoV-2 transcriptome should be different from traditional SNV identification. J Appl Genet 2022; 63:587-594. [PMID: 35661108 PMCID: PMC9166928 DOI: 10.1007/s13353-022-00706-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 10/31/2022]
Affiliation(s)
- Houhao Cai
- Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Xiantao Liu
- Pulmonary and Critical Care Medicine, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Xin Zheng
- Department of Respiratory and Critical Care Medicine, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, 266000, Shandong, China.
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9
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An evolutionarily conserved mechanism that amplifies the effect of deleterious mutations in osteosarcoma. Mol Genet Genomics 2022; 297:373-385. [DOI: 10.1007/s00438-021-01852-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
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10
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Li J, Yu CP, Li Q, Chang S, Xie LL, Wang S. Large-scale omics data reveal the cooperation of mutation-circRNA-miRNA-target gene network in liver cancer oncogenesis. Future Oncol 2021; 18:163-178. [PMID: 34677082 DOI: 10.2217/fon-2021-0940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aims: Clarifying the initial trigger of the differentially expressed genes in cancers helps researchers understand the cellular system as a whole network. Materials & methods: We retrieve the transcriptome and translatome of tumor and normal tissues from ten liver cancer patients and define differentially expressed genes and tumor-specific mutations. We associate the oncogenesis with the mutations by target prediction and experimental verification. Results: Upregulated genes have tumor-specific mutations in 3'UTRs that abolish the binding of miRNAs. For downregulated genes, their corresponding miRNAs are mutually targeted by two circRNAs, with mutations in base-pairing regions. Transfection experiments support the oncogenic role of these mutations. Conclusions: The tumor-specific mutations serve as the initial trigger of liver cancer. The mutation-circRNA-miRNA-target gene chain is completed.
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Affiliation(s)
- Jian Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Chun-Peng Yu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Qun Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Shuai Chang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Ling-Ling Xie
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Song Wang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
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Chu D, Wei L. Direct in vivo observation of the effect of codon usage bias on gene expression in Arabidopsis hybrids. JOURNAL OF PLANT PHYSIOLOGY 2021; 265:153490. [PMID: 34375820 DOI: 10.1016/j.jplph.2021.153490] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Hybrids are the perfect materials to study cis regulatory elements because the two parental alleles are subjected to identical trans environments. There has been a debate on whether synonymous codon usage could affect gene expression. In vitro experiments found that luciferase genes with enhanced codon optimality showed elevated mRNA expression. However, the underlying mechanism is still unclear, and no direct evidence is observed to support this notion. By mapping the RNA-seq data of hybrids of Arabidopsis thaliana and Arabidopsis lyrata, we quantified the allele-specific reads and estimated the relative expression of orthologous genes. We focused on orthologous genes with dN = 0 and dS > 0, which means that they only differ in synonymous codon usage. We found that orthologous genes with higher codon optimality in A. thaliana tend to have higher expression levels of the A. thaliana allele. Codon usage bias could influence gene expression. This phenomenon is not only found in in vitro experiments but also supported by in vivo observations. Therefore, synonymous mutations could have a broad impact from multiple aspects and should not be automatically ignored in genomic studies. KEY MESSAGE: In Arabidopsis hybrids, alleles with higher codon optimality tend to have higher expression levels.
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Affiliation(s)
- Duan Chu
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China
| | - Lai Wei
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.
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12
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Mutation profiling of a limbless pig reveals genome-wide regulation of RNA processing related to bone development. J Appl Genet 2021; 62:643-653. [PMID: 34278546 DOI: 10.1007/s13353-021-00653-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
Mutation is the basis of phenotypic changes and serves as the source of natural selection. The development of limbs has been the milestone in vertebrate evolution. Several limb and bone-related genes were verified experimentally, but other indirect and regulatory factors of limb development remained untested, especially very few cases were observed in natural environment. We report a naturally born serpentized pig without hindlimbs. Whole genome sequencing followed by comparative genomic analysis revealed multiple interesting patterns on the handicapped pig-specific mutations. Although the bone-related genes are not directly subjected to mutations, other regulatory factors such as the RNA deaminase genes Adar are damaged in the handicapped pig, leading to the abolished A-to-I deamination in many functional, conserved genes as well as the bone-related genes. This is a precious case that the limbless phenotype is observed in naturally born non-model organisms. Our study broadened the generality of the limbless phenotype across mammals and extended the regulation of hindlimb development to other non-bone-related genes. Our knowledge of limb and bone-related mutations and regulation would also contribute to human genetics.
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13
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Chu D, Wei L. Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana. BMC Ecol Evol 2021; 21:68. [PMID: 33910528 PMCID: PMC8079846 DOI: 10.1186/s12862-021-01792-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 04/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Synonymous mutations do not alter the amino acids and therefore are regarded as neutral for a long time. However, they do change the tRNA adaptation index (tAI) of a particular codon (independent of its context), affecting the tRNA availability during translation. They could also change the isoaccepting relationship with its neighboring synonymous codons in particular context, which again affects the local translation process. Evidence of selection pressure on synonymous mutations has emerged. RESULTS The proposed selection patterns on synonymous mutations are never formally and systematically tested in plant species. We fully take advantage of the SNP data from 1,135 A. thaliana lines, and found that the synonymous mutations that increase tAI or the isoaccepting mutations in isoaccepting codon context tend to have higher derived allele frequencies (DAF) compared to other synonymous mutations of the opposite effects. CONCLUSIONS Synonymous mutations are not strictly neutral. The synonymous mutations that increase tAI or the isoaccepting mutations in isoaccepting codon context are likely to be positively selected. We propose the concept of context-dependent and -independent selection on synonymous mutations. These concepts broaden our knowledge of the functional consequences of synonymous mutations, and should be appealing to phytologists and evolutionary biologists.
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Affiliation(s)
- Duan Chu
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian, Beijing, China
| | - Lai Wei
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian, Beijing, China.
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14
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Dai D, Ma Z, Song R. Maize kernel development. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:2. [PMID: 37309525 PMCID: PMC10231577 DOI: 10.1007/s11032-020-01195-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/03/2020] [Indexed: 06/14/2023]
Abstract
Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444 China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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